Update .gitea/workflows/deploy-pages.yml

change action trigger to default branch name

.gitea/workflows/deploy-pages.yml

@@ -0,0 +1,44 @@
+name: Build and Deploy Documentation
+
+on:
+  push:
+    branches:
+      - root6
+  workflow_dispatch:
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    container:
+      image: gitea.psi.ch/images/alpine-jupyterbook
+    steps:
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install system dependencies
+        run: |
+          apk add doxygen graphviz
+
+      - name: Build musrfit-tech-docu
+        run: |
+          cd doc
+          mkdir technical 
+          doxygen musrfit_dox.cfg
+          doxygen musredit_qt5_dox.cfg
+          doxygen mupp_qt5_dox.cfg
+
+      - name: Configure Git
+        run: |
+          git config --global user.name "Gitea Actions"
+          git config --global user.email "actions@gitea.local"
+
+      - name: Push to gitea-pages branch
+        run: |
+          git checkout --orphan gitea-pages
+          git reset --hard
+          cp -r ./doc/technical/html/* .
+          git add .
+          git commit -m "Deploy site"
+          git push -f https://${{secrets.GITHUB_TOKEN}}@gitea.psi.ch/${{ github.repository }}.git gitea-pages
+

.gitignore

@@ -0,0 +1,2 @@
+# ignore all files generated from an in-repo build
+build/

CMakeLists.txt

@@ -1,7 +1,7 @@
 # - musrfit
 cmake_minimum_required(VERSION 3.17)
 
-project(musrfit VERSION 1.9.0 LANGUAGES C CXX)
+project(musrfit VERSION 1.9.9 LANGUAGES C CXX)
 
 #--- musrfit specific options -------------------------------------------------
 option(nexus "build optional NeXus support. Needed for ISIS" OFF)
@@ -109,13 +109,13 @@ find_package(FFTW3 REQUIRED)
 find_package(LibXml2 REQUIRED)
 
 #--- check for OpenMP ---------------------------------------------------------
-if (try_OpenMP AND NOT APPLE)
+if (try_OpenMP)
   find_package(OpenMP)
-  if (OpenMP_FOUND)
+  if (OpenMP_CXX_FOUND)
     add_definitions(-DHAVE_GOMP)
     set(HAVE_GOMP 1 CACHE INTERNAL "Have GOMP")
-  endif (OpenMP_FOUND)
-endif (try_OpenMP AND NOT APPLE)
+  endif (OpenMP_CXX_FOUND)
+endif (try_OpenMP)
 
 #--- check for Qt -------------------------------------------------------------
 if (qt_based_tools)
@@ -200,8 +200,10 @@ endif (qt_based_tools)
 
 #--- if NeXus check also for HDF4, HDF5, and MXML -----------------------------
 if (nexus)
-  find_package(HDF5 COMPONENTS CXX REQUIRED )
-  find_package(HDF4 REQUIRED)
+  find_package(HDF5 COMPONENTS CXX REQUIRED)
+  if (HAVE_HDF4)
+    find_package(HDF4 REQUIRED)
+  endif (HAVE_HDF4)  
   find_package(NEXUS REQUIRED)
   add_definitions(-DPNEXUS_ENABLED)
 endif (nexus)
@@ -222,10 +224,48 @@ else ()
   set(IS_GIT_REPO 0)
 endif ()
 
+#--- start create git-revision.h ----------------------------------------------
+if (IS_GIT_REPO)
+  execute_process(COMMAND sh ${CMAKE_SOURCE_DIR}/src/git_revision.sh)
+
+  set(HAVE_GIT_REV_H "-DHAVE_GIT_REV_H")  
+  set(GIT_REV_H "git-revision.h")
+else (IS_GIT_REPO)
+  set(HAVE_GIT_REV_H "")  
+  set(GIT_REV_H "")
+endif (IS_GIT_REPO)
+
+#--- end create git-revision.h ------------------------------------------------
+
+#--- rpath related things -----------------------------------------------------
+# use, i.e. don't skip the full RPATH for the build tree
+set(CMAKE_SKIP_BUILD_RPATH FALSE)
+
+# when building, don't use the install RPATH already
+# (but later on when installing)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+
+# add the automatically determined parts of the RPATH
+# which point to directories outside the build tree to the install RPATH
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+# the RPATH to be used when installing, but only if it's not a system directory
+list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
+if("${isSystemDir}" STREQUAL "-1")
+    set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+endif("${isSystemDir}" STREQUAL "-1")
+set(rpath ${CMAKE_INSTALL_RPATH})
+string(APPEND rpath ";/usr/local/lib")
+set(CMAKE_INSTALL_RPATH "${rpath}")
+
 #--- propagate to the sub-directories -----------------------------------------
 add_subdirectory(src)
 
 #--- write summary of the installation
+cmake_host_system_information(RESULT PROCESSOR QUERY PROCESSOR_DESCRIPTION)
+
 message("")
 message("|-----------------------------------------------------------------------|")
 message("|                                                                       |")
@@ -233,8 +273,9 @@ message("|                            Summary
 message("|                                                                       |")
 message("|-----------------------------------------------------------------------|")
 message("")
-message(" System: ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
-message(" -------")
+message(" System:    ${CMAKE_HOST_SYSTEM_NAME} ${CMAKE_SYSTEM_PROCESSOR} - ${CMAKE_HOST_SYSTEM_VERSION}")
+message(" Processor: ${PROCESSOR} (${CMAKE_SYSTEM_PROCESSOR})")
+message(" ----------")
 message("")
 message(" musrfit Version: ${musrfit_VERSION}")
 message(" ----------------")
@@ -260,7 +301,11 @@ endif (OpenMP_FOUND)
 
 if (nexus)
   message("")
-  message(" HDF4    found in ${HDF4_INCLUDE_DIRS}")
+  if (HAVE_HDF4)
+    message(" HDF4    found in ${HDF4_INCLUDE_DIRS}")
+  else (HAVE_HDF4)
+    message(" HDF4    not present.")	  
+  endif (HAVE_HDF4)	  
   message(" HDF5    found in ${HDF5_INCLUDE_DIRS}, Version: ${HDF5_VERSION}")
   message(" NeXus   found in ${NEXUS_INCLUDE_DIR}, Version: ${NEXUS_VERSION_STRING}")
 endif (nexus)

ChangeLog

@@ -12,6 +12,54 @@ or
 
 https://bitbucket.org/muonspin/musrfit/commits/all
 
+Release of V1.9.9, 2025/06/08
+=============================
+
+add THEORY functions for local Gaussian / global Lorentzian, and a simple F-mu-F function.
+
+Release of V1.9.8, 2025/03/24
+=============================
+
+add a user interface option to export data from a msr-file view (single- or multiple files).
+
+Release of V1.9.7, 2025/01/18
+=============================
+
+allow spaces in RUN block path-filename
+
+Release of V1.9.6, 2024/12/02
+=============================
+
+added jump to block feature in musredit.
+
+
+Release of V1.9.5, 2024/06/24
+=============================
+
+yaml export of ALL fit-parameters, as initiated by R.M.L. McFadden.
+
+Release of V1.9.4, 2024/06/08
+=============================
+
+enable OpenMP for macOS.
+
+Release of V1.9.3, 2024/04/19
+=============================
+
+fix of function string generation from AST.
+
+Release of V1.9.2, 2023/10/25
+=============================
+
+switch over to smart pointers wherever possible.
+
+Release of V1.9.1, 2023/05/16
+=============================
+
+add option [-c, --count] to dump_header which will dump the number of counts
+per detector and the total number of counts. Currently for MusrRoot data format
+only. For the other data formats it will be implement asap
+
 Release of V1.9.0, 2023/02/17
 =============================
 

README.md

@@ -32,7 +32,6 @@ For a more exhaustive user documentation see:
 
 <andreas.suter@psi.ch>
 
-For the beta-NMR related parts, please contact
-
+For the beta-NMR related parts, please contact Zaher Salman
 <zaher.salman@psi.ch>
 

cmake/FindFFTW3.cmake

@@ -75,7 +75,7 @@ endfunction()
 #as35 endif()
 
 find_path(FFTW3_INCLUDE NAMES fftw3.h
-  HINTS "/usr/include" "/opt/local/include"
+  HINTS "/usr/include" "/opt/local/include" "/app/include"
 )
 
 find_library(FFTW3_LIBRARY fftw3)

cmake/configure_musrfit_version_file.cmake.in

@@ -1,30 +0,0 @@
-# configure_musrfit_version_file.cmake.in:
-set(SRC_DIR "@CMAKE_SOURCE_DIR@")
-set(BIN_DIR "@CMAKE_CURRENT_BINARY_DIR@")
-
-# Set variables
-set(CMAKE_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@")
-set(MUSRFIT_VERSION "@MUSRFIT_VERSION@")
-
-# Get the current working branch
-execute_process(
-  COMMAND git rev-parse --abbrev-ref HEAD
-  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-  OUTPUT_VARIABLE GIT_BRANCH
-  OUTPUT_STRIP_TRAILING_WHITESPACE
-)
-
-# Get the latest abbreviated commit hash of the working branch
-execute_process(
-  COMMAND git log -1 --pretty="%h, %ci"
-  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
-  OUTPUT_VARIABLE GIT_CURRENT_SHA1
-  OUTPUT_STRIP_TRAILING_WHITESPACE
-)
-
-configure_file(
-  ${SRC_DIR}/cmake/git-revision.h.in
-  ${BIN_DIR}/git-revision.h
-  @ONLY
-)
-# EOF

doc/examples/DepthProfiles/1300Ar/depth_profile_startup.xml

@@ -1,35 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<nonlocal xmlns="http://nemu.web.psi.ch/musrfit/nonlocal">
+<depthProf xmlns="http://nemu.web.psi.ch/musrfit/depthProf">
     <comment>
         TrimSp information
     </comment>
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>SiC_1300x_52nm_48nm_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
     </trim_sp>
-</nonlocal>
+</depthProf>

doc/examples/DepthProfiles/1300x/depth_profile_startup.xml

@@ -1,35 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<nonlocal xmlns="http://nemu.web.psi.ch/musrfit/nonlocal">
+<depthProf xmlns="http://nemu.web.psi.ch/musrfit/depthProf">
     <comment>
         TrimSp information
     </comment>
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>SiC_1300x_52nm_48nm_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
     </trim_sp>
-</nonlocal>
+</depthProf>

doc/examples/DepthProfiles/PECVD_Si/depth_profile_startup.xml

@@ -1,35 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<nonlocal xmlns="http://nemu.web.psi.ch/musrfit/nonlocal">
+<depthProf xmlns="http://nemu.web.psi.ch/musrfit/depthProf">
     <comment>
         TrimSp information
     </comment>
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>Si10_2.0_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
     </trim_sp>
-</nonlocal>
+</depthProf>

doc/examples/DepthProfiles/PECVD_thermal_SiC/depth_profile_startup.xml

@@ -1,35 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<nonlocal xmlns="http://nemu.web.psi.ch/musrfit/nonlocal">
+<depthProf xmlns="http://nemu.web.psi.ch/musrfit/depthProf">
     <comment>
         TrimSp information
     </comment>
     <trim_sp>
         <data_path>./TRIMSP/</data_path>
         <rge_fln_pre>SiO2_70nm2.0_30nm2.2_SiC_E</rge_fln_pre>
-        <energy_list>
-            <energy>1000</energy>
-            <energy>2000</energy>
-            <energy>3000</energy>
-            <energy>4000</energy>
-            <energy>5000</energy>
-            <energy>6000</energy>
-            <energy>7000</energy>
-            <energy>8000</energy>
-            <energy>9000</energy>
-            <energy>10000</energy>
-            <energy>11000</energy>
-            <energy>12000</energy>
-            <energy>13000</energy>
-            <energy>14000</energy>
-            <energy>15000</energy>
-            <energy>16000</energy>
-            <energy>17000</energy>
-            <energy>17000</energy>
-            <energy>18000</energy>
-            <energy>19000</energy>
-            <energy>20000</energy>
-            <energy>21000</energy>
-            <energy>22000</energy>
-        </energy_list>
+        <energy_vect start="1000" stop="22000" step="1000"/>
     </trim_sp>
-</nonlocal>
+</depthProf>

doc/examples/UserFcn/PUserFcn.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2025 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

doc/examples/UserFcn/PUserFcn.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2021 by Andreas Suter                              *
+ *   Copyright (C) 2007-2025 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

doc/examples/test-histo-ROOT-NPP.msr

@@ -15,9 +15,6 @@ asymmetry      3
 simplExpo      4          (rate)
 TFieldCos      1     2       (phase frequency)
 
-###############################################################
-#FUNCTIONS
-
 ###############################################################
 RUN data/lem08_his_2279 MUE4 PSI ROOT-NPP   (name beamline institute data-file-format)
 fittype         0         (single histogram fit)
@@ -39,6 +36,14 @@ MINIMIZE
 MINOS
 SAVE
 
+###############################################################
+FOURIER
+units            Gauss   # units either 'Gauss', 'Tesla', 'MHz', or 'Mc/s'
+fourier_power    10
+apodization      STRONG  # NONE, WEAK, MEDIUM, STRONG
+plot             POWER   # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL
+dc-corrected     true
+
 ###############################################################
 PLOT 0   (single histo plot)
 runs     1   

doc/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 429dcaf60d751fc64b55c07d7174ea6f
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: a49a5e0b750ed752f738f66d3ddeadd4
 tags: 645f666f9bcd5a90fca523b33c5a78b7

doc/html/_images/musrview2dat.svg

@@ -0,0 +1,259 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   width="22"
+   height="22"
+   viewBox="0 0 22.000001 22"
+   id="svg2"
+   version="1.1"
+   inkscape:version="1.0.2 (e86c870879, 2021-01-15)"
+   sodipodi:docname="musrview2dat-plain.svg">
+  <defs
+     id="defs4">
+    <marker
+       inkscape:stockid="Arrow1Sstart"
+       orient="auto"
+       refY="0.0"
+       refX="0.0"
+       id="Arrow1Sstart"
+       style="overflow:visible"
+       inkscape:isstock="true">
+      <path
+         id="path8245"
+         d="M 0.0,0.0 L 5.0,-5.0 L -12.5,0.0 L 5.0,5.0 L 0.0,0.0 z "
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+         transform="scale(0.2) translate(6,0)" />
+    </marker>
+    <marker
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